Scared To Lose It All
by battleshipxx101
Summary: "What's gonna happen to me?" Skye asked him. A story set after "Seeds" DISCLAIMER: I do not own Marvel's Agents of S.H.I.E.L.D.
1. Chapter 1

"What's gonna happen to me?" Skye asked him.

"Excuse me?" Coulson said, confused.

"Come on, AC. I'm basically an alien. An 0-8-4." She crossed her arms and looked at him expectantly. They were in his office after the events of the mission at the Academy.

Coulson sighed. Skye tried again, "What's SHIELD gonna do to me? Are they gonna put me in a place like the sandbox or something? Keep me contained?" She tried to hide the fear and worry in her voice, but Coulson could see right through it.

"I don't know yet, Skye. I don't know how much Director Fury knows about you and your case."

Skye felt her eyes water. She didn't want to leave the bus. She became used to all this–people caring for each other, being together, having happy moments, and everything there is. She became used to having being in this team–this family. And the last thing she wanted was to be separated from them.

"I'm sorry, Skye." Coulson said.

"You have to stop apologizing, AC." She smiled. "I already told you, it's not something to be sorry for."

Coulson looked at her sadly. He really didn't know how much SHIELD knew. How much of Skye's life did they write for her? Skye leaving and returning back to the orphanage throughout her whole life was SHIELD's work. Was it also them who planned for Skye to live in a van? To join SHIELD? To be part of this team?

"We don't know a lot of things. But here's what I do know–we're not letting you go no matter what. You're a part of this team. You stay here with us no matter what."

Skye smiled at what he said. "Thank you, AC."

Coulson smiled back. "If anything comes up, I'll tell you."

Skye nodded before she left Coulson's office. She felt good at hearing Coulson say those words, but even with them, she still couldn't help but feel worried, scared and sad. Still with a mind full of thoughts, Skye made her way to her bunk. She didn't notice Ward sitting on one of the sofas in the lounge.

"Hey," he said to her, but Skye didn't turn around to face him. She continued to walk into her bunk. Ward grew confused. He placed his book down and followed his rookie inside her bunk. He saw her sitting down on the side of her bed, head in her hands and looking down.

"Skye?" He said. She looked up and Ward saw the tears threatening to fall from her eyes. He immediately closed the door and sat beside her.

"What's the matter?" He asked, but she remained silent. "Wanna talk about it?" He tried again, but she shook her head no. Ward sighed. He didn't like seeing her like this. Skye was always a cheerful and bubbly person. It took a lot of weight to bring her spirits down, and seeing her like this gave him the message that she was going through a really bad time– so bad that she, the girl who doesn't let anything bring her down, was crying. Yet, he didn't know what he could say. He didn't expect Skye to turn down his offer to talk, but knew he needed to respect that give her space. If Skye didn't want to talk, there was only one other option.

Gently, Ward placed his arm around Skye's shoulders and pulled her close against him. Skye tensed up at first, but soon began to relax.

Minutes passed by. Skye cried and Ward held her, patiently waiting for when she's ready to open up. Skye didn't feel herself move until she felt her back lying on the soft mattress. Ward didn't separate from her as he lied the both of them down on the bed. When he did, he pulled her closer until Skye's head was resting on his chest. He placed his left arm on her as the other encircled her waist. She placed one arm on Ward's stomach and they continued to hold on to each other. Neither of them spoke all this time. A few more minutes passed by and Ward heard Skye softly snoring. Her breathing was now more relaxed. He looked at her face. There were dry tears on her now puffy cheeks. Ward tucked a strand of her hair behind her ear and sighed. He didn't know what was going on with his rookie right now. He hasn't spoken about it but he already saw that she's been different since the mission at the Academy. He had no clue what happened to her. But he vowed to be there for her through all this.


	2. Chapter 2

**Author's Note: Hi everyone! I meant to post this earlier but school work was really taking up my time. I watched the latest episode today and I don't even know how I can survive a whole month without AOS, especially after that cliffhanger. I wish everyone good luck for the next four weeks. Stay strong. **

**Here's the next chapter. I hope you like it! :) :)**

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**DISCLAIMER: I DO NOT OWN MARVEL'S AGENTS OF S.H.I.E.L.D.**

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Chapter 2:

There was a knock in the door. Coulson looked up from his paperwork and said, "Come in."

He watched as Agent Ward stepped towards his desk.

"Are you busy, sir?"

"No, not really. What's on your mind, Agent Ward?"

"Skye," Ward answered. "As soon as she left your office and went downstairs, she started crying. I want to know what happened. What's bothering her?"

Coulson hesitated. He bit the inside of his lower lip and he had a look of uncertainty.

"Sir," Ward addressed him again. "I'm her S.O. I think I'm entitled to know if something's wrong with my rookie, especially since she hasn't been the same since our last mission."

"No, she hasn't." Coulson frowned. He seemed to be deciding on something in his mind.

"Then please tell me what's wrong. Maybe I can help." Ward stared at Coulson. He was determined to find out what happened with Skye. He couldn't stand seeing her in that state. He needed to do something about it.

Coulson sighed, then looked at his wrist watch. _11:25 pm. _"Where is she?"

"In her bunk. She fell asleep half an hour ago." Ward said. Coulson stood up.

"Call the others to the briefing room. Tell them it's important."

Ward nodded again, then went out of Coulson's office. Before heading to the lab, he passed by Skye's bunk and made sure she was still sleeping. He saw her facing the wall and hugging a pillow. The blanket reached only her ankles. Ward moved closer and gently grabbed the blanket. He stretched it until it covered Skye's elbows. Then, he went out and headed to the lab. As soon as he entered it, he is greeted by the science duo.

"Hello Agent Ward." Simmons said without looking at him. She was focused on the holographic image in front of her.

"Briefing room." Ward said. That made the duo look at him in both confusion and disbelief. It wasn't often that they would get brief at this time

"It's important." He told them. Fitzsimmons nodded and did a few things on their gadgets before following Ward upstairs.

"Something wrong, Agent Ward?" Fitz asked.

"Keep it down. Skye's sleeping."

"Oh, she won't be joining us then?" Simmons asked. Ward gave them one look that made them understand that there was a reason why they were being called at this time.

When they all piled inside, they saw Coulson holding a file folder. May stood at the side of the room. They looked expectantly at Coulson.

"I know it's a little late for a briefing, but circumstance calls for it." Coulson looked at the file in his hands before continuing. "You all remember our particular mission involving Skye and Miles Lydon. When I called Skye to my office then, I asked her to give me a good enough reason to let her stay here. She revealed to me her real reason for joining the Rising Tide–for targeting SHIELD." Coulson clicked the table and there appeared a file. "This is Skye's only file about herself. She wanted to know where she came from, and all she got was a document recording her transfer to St. Agnes Orphanage when she was a baby."

The others stared at the redacted file in front of them.

"This is the reason," Coulson continued. "Why she targeted SHIELD. We did that to her. And she wanted to know why. She asked me to look into it and I did. Agent May and I found a mission report involving the agent who was responsible for erasing that file." He clicked something again and picture appeared. Apart from Agent May and Coulson, all the others were shocked. Ward and Fitz's jaws were slightly hanging open. Simmons covered her mouth with her hand.

"This is Agent Avery. She, along with a team of agents, was sent to retrieve an 0-8-4. When they did, it turns out they weren't the ones interested in it. A whole village plus an entire SHIELD team died protecting the 0-8-4. Agent Avery and her partner, Agent Lumley survived. They took the object from the head agent's arms. He was dead. They thought the bloody 0-8-4 was dead too, but she was only sleeping–"

"Whoa, whoa. What do you mean–" Ward was cut off in speech.

"The 0-8-4 was a baby girl."

"What– Skye?" Ward became speechless. Fitz was stunned into silence as well. Simmons opened and closed her mouth in shock. She started to tear up. No one spoke among them. Coulson looked remorseful. Even May showed a little of it too. But Coulson wasn't done.

"Agent Avery decided it best to erase her from existence. No files. No data. She invented the Foster System Protocol to hide the girl. She made sure that the kid was rotated every few months."

"While you were in the Academy, May and I tracked down Agent Lumley. That's how we found out. He even told us everything. I told Skye eventually. Lumley said to stay away from her."

Because of that statement, he received looks of disbelief and outrage. "But I don't plan on kicking her off this bus at any cost. Skye's a member of this team. Before anything else, she's part of us. And we're going to do everything to make sure she stays safe and hidden."

They all nodded in agreement.

"I ask for another thing. Don't let Skye feel like we're treating her any different. She's already carrying a heavy burden inside. The last thing we want is for her to run away." Coulson said.

Ward's chest tightened at the thought. He couldn't–_wouldn't_ let Skye leave. He had to keep her safe. She needed him now more than ever.

After murmurs of, "Of course," from FitzSimmons, Coulson dismissed them. Ward stayed. But before he could say anything, Coulson beat him to it.

"I know what you're thinking, Ward. Of course we will do anything to protect Skye. You don't need to doubt it."

"I don't, sir. I know you will. I just have one more question."

Coulson looked at him expectantly.

"What happens to her? What will SHIELD do?"

Coulson remained quiet for a moment. "She asked me the same thing earlier. She went to my office and asked me that too. I know she tried to look strong and all in front of me, but, I could see she's afraid."

"Of course she is." Ward muttered.

"I'll tell you the same thing I told her– I don't know what S.H.I.E.L.D. knows. But I do think they have no clue that the girl they erased from existence sits here on our Bus. I plan to keep it that way. I want her protected just as much as you do."

"I understand, sir."

Coulson turned the screens off and started to move towards the door.

"And Ward?"

"Sir?"

"She doesn't know that I told you."

Ward nodded in understanding.

"Good night, sir."

"Good night." Coulson then went out of the room. Ward stared at the black screen in front of him. He could see his own reflection from it. Ward needed a moment to process all of this. He couldn't help but picture how Skye was found– bloody and helpless. Ward knew what he had to do. He wasn't used to feeling like this–wanting to protect someone other than himself. For years, he worked alone. Now, he had a team. He had people he has grown to care about. He had Skye. She's always been something else. She brought out the best in him. She made this family closer through her bubbly and cheerful personality.

Ward was confused and worried. This was no ordinary revelation. They all thought Skye was just a regular hacker. And now they found out that she was an 0-8-4. What happens to her then? What if someone decides to take her away from them? From him? He couldn't let anything happen to her. Not after this. The entire time, no one was aware of the truth about Skye. And now that they do, what will happen? Can they protect her? What if she doesn't want to be protected? Knowing Skye, Ward was sure she would want to keep everyone else away from her for their safety. That was the tough part.

Ward ran his hand through his hair. Then he went out into the lounge. Though he was tired, his mind was too full to shut down. He stood in front of his bunk door, but he didn't go in. He stared at another door– _her _door. There was something inside him that made it hard to stay away from her. There was this feeling inside that was urging Ward to be as near as possible to his rookie. Quietly, he went near her bunk. He gently opened the door and peeked. He saw Skye cuddling a pillow. Her face was still slightly puffy. Her hair was strewn all over her pillow. Ward smiled sadly at the sight. He felt proud of his rookie. She's been working hard in everything she did. She was always there for the whole team. She deserved to be happy. But then again, all she wanted was the truth. She wanted answers. And now that she had them, it may just destroy her.

Ward frowned. _Poor Skye._ Then, sighing to himself, he closed the bunk door and made his way to his own bed. When he lied down, however, it didn't seem like sleep was going to overcome him anytime soon. He had arms tucked under his head. He stared at the ceiling as he let thousands of thoughts swim through his mind. Before he realized it, an entire hour has passed. It was already 1:37 when he looked at his clock.

Ward sat up. He was about to change into more comfortable sleeping clothes when a high-pitched sound made him stop. He knew that voice from anywhere, and he knew that cry. Within seconds, Ward was out of his bunk.

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**A/N: I'll be posting the last chapter for this hopefully very soon. I still need to finish writing it. :) :)**


	3. Chapter 3

**A/N: This would be the last chapter! :) I hope you enjoyed reading this story. I'd be focusing on my other fic now so, if you're interested, check it out. :) Thanks for reading!**

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**DISCLAIMER: I DO NOT OWN MARVEL'S AGENTS OF S.H.I.E.L.D.**

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Skye's POV

_I was standing in the makeshift gym for some reason. There were two SHIELD vans right outside of the cargo hold. Then, the agents came out. I could see at least a dozen or so. Three of them started to approach me. I felt my heartbeat go faster. Where was everyone? Where was Coulson? Where was Grant? I was starting to panic now._

_"You need to come with us," said the agent in front of me in a monotonous voice._

_"What? Where?" I asked frantically._

_"You have been deemed dangerous to this team. We need to bring you to Headquarters." They grabbed me by the arms._

_"No, wait. Coulson! Cou–"_

_"They can't help you."_

_"No, wait! Please–"_

_As I struggled, I turned around and saw Coulson and May arrive. They saw what was happening and quickly went down, wearing looks of shock._

_"What is going on!?" Coulson demanded._

_"Let go of the girl." May said forcefully._

_"We can't do that, ma'am. We have orders from Director Fury." They started to pull me towards the vans. _

_No. No. I can't leave._

_I saw FitzSimmons hurriedly go out of the lab to find out what was going on._

_"Orders to do what exactly!?" Coulson shouted as he hurriedly followed me as I was dragged. I almost feared Grant wasn't going to show up. But there he appeared on the catwalk, looking outraged. I looked at his eyes though my vision was getting blurry because of the tears._

_"That's classified." The agents then pushed me inside the van._

_"No, please–" I cried. Through the window, I saw Grant run towards me, but the van quickly drove off. _

_"Please, I haven't even said goodbye!" I told the agent in the passenger seat._

_"We had orders to collect you as soon as possible, in any way we had to." He answered with an emotionless tone._

_I cried and cried as I looked out the window. I didn't even get a chance to say goodbye properly. Not to FitzSimmons. Not to May or Coulson. And especially not to Grant._

_"Please, please take me back!" I demanded. They did nothing but ignore me. I was furious now. I kept shouting, "TAKE ME BACK! TAKE ME BACK!" My vision was starting to cloud. Before everything disappeared, I heard a voice._

_"Skye! Skye! Wake up!"_

I bolted right up. I felt cold sweat dripping from my face. I looked around and saw Grant leaning over me, looking concerned. I didn't even say anything. I started crying again and I felt Grant pull me into his arms.

"Shhh, it's okay. Skye, it's okay." He whispered to me while rubbing circles on my back.

"Don't let them take me away. Don't let them take me away." I said in between sobs.

"Shhh, no one's gonna take you away, Skye. I promise you. You're not going anywhere. I won't let anyone take you." He said.

"I wanna stay here." I said while still crying.

"And you will. I won't let anything happen to you, okay?" Grant said. I nodded against his chest.

"You need to calm down. Just breathe, okay? In...Out..."

After a few moments of that, I relaxed against him, but didn't stop crying. He rubbed my back as he continued to whisper soothing words in my ear. I was glad that Grant came. He always made me feel safe no matter what. He was the only one who could do that. Growing up alone, I was used to finding comfort from myself only. But now, I had been given a team. A family. And I had Grant.

A few more minutes passed until I pulled away. Grant still looked worried.

"What happened?" He asked softly.

"Nightmare." I answered, though I kept my head down.

"You wanna talk about it?"

I looked at his eyes which were full of concern. There was a knowing look there and my gut told me to ask.

"You know, don't you?" I asked quietly. He nodded. _Oh no...What does Grant think of me now?_

I kept my head down and let a few tears escape. Then, Grant lifted my chin with his fingers.

"Skye," he started.

"Are you scared?" I asked.

"The only thing I'm afraid of is failing to protect you, Skye. I'm afraid that I won't be able to do enough to keep you safe."

My heart melted at his words. _He cares about me._

"But–"

"But nothing. Don't even think about what SHIELD can do. What's important is what _we_ can do. This team. Me. We will do everything to make sure you're safe here with us, not in some isolated containing room, but _here_ with me. I promise you that, Skye." He wiped my tears off and cupped my face. "Trust me."

Then he leaned forward and kissed my forehead. When he pulled away, I was afraid he would leave. But instead he asked, "Do you want me to stay with you?" I nodded and he smiled at me. I lied back down and he lied right next to me. He wrapped his arms around me and I pressed my face against his chest. He pulled me closer and I slowly drifted off to sleep. I felt Grant kiss the top of my head, and the last thing I heard from him was, "I'll always be here to protect you."

END

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**A/N: So...there you are! :) I hope you liked it and thank you again, for reading! xx**


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